| /dports/science/cdk/cdk-cdk-2.3/base/test-standard/src/test/java/org/openscience/cdk/stereo/ |
| H A D | CyclicCarbohydrateRecognitionTest.java | 164 m.getAtom(1), m.getAtom(0), m.getAtom(9), m.getAtom(2)); in betaDGlucose_Haworth()
168 m.getAtom(10), m.getAtom(1), m.getAtom(2), m.getAtom(3)); in betaDGlucose_Haworth()
172 m.getAtom(3), m.getAtom(2), m.getAtom(11), m.getAtom(4)); in betaDGlucose_Haworth()
176 m.getAtom(6), m.getAtom(3), m.getAtom(4), m.getAtom(5)); in betaDGlucose_Haworth()
180 m.getAtom(7), m.getAtom(5), m.getAtom(0), m.getAtom(1)); in betaDGlucose_Haworth()
226 m.getAtom(8), m.getAtom(0), m.getAtom(1), m.getAtom(2)); in betaDGlucose_Chair()
230 m.getAtom(7), m.getAtom(2), m.getAtom(3), m.getAtom(4)); in betaDGlucose_Chair()
234 m.getAtom(4), m.getAtom(3), m.getAtom(6), m.getAtom(5)); in betaDGlucose_Chair()
238 m.getAtom(11), m.getAtom(4), m.getAtom(5), m.getAtom(0)); in betaDGlucose_Chair()
242 m.getAtom(0), m.getAtom(5), m.getAtom(10), m.getAtom(1)); in betaDGlucose_Chair()
[all …]
|
| /dports/science/cdk/cdk-cdk-2.3/storage/smiles/src/test/java/org/openscience/cdk/smiles/ |
| H A D | BeamToCDKTest.java | 281 …assertThat(tc.getLigands(), is(new IAtom[]{ac.getAtom(1), ac.getAtom(3), ac.getAtom(4), ac.getAtom… in _2R_butan_2_ol()
302 …assertThat(tc.getLigands(), is(new IAtom[]{ac.getAtom(1), ac.getAtom(3), ac.getAtom(4), ac.getAtom… in _2S_butan_2_ol()
332 …assertThat(tc1.getLigands(), is(new IAtom[]{ac.getAtom(0), ac.getAtom(2), ac.getAtom(6), ac.getAto… in tetrahedralRingClosure()
342 …assertThat(tc2.getLigands(), is(new IAtom[]{ac.getAtom(1), ac.getAtom(5), ac.getAtom(7), ac.getAto… in tetrahedralRingClosure()
361 assertThat(dbs.getStereoBond(), is(ac.getBond(ac.getAtom(1), ac.getAtom(2)))); in e_1_2_difluroethene()
363 …is(new IBond[]{ac.getBond(ac.getAtom(0), ac.getAtom(1)), ac.getBond(ac.getAtom(2), ac.getAtom(3))}… in e_1_2_difluroethene()
384 …is(new IBond[]{ac.getBond(ac.getAtom(0), ac.getAtom(1)), ac.getBond(ac.getAtom(2), ac.getAtom(3))}… in z_1_2_difluroethene()
405 …is(new IBond[]{ac.getBond(ac.getAtom(0), ac.getAtom(1)), ac.getBond(ac.getAtom(3), ac.getAtom(4))}… in e_1_2_difluroethene_explicit()
427 …is(new IBond[]{ac.getBond(ac.getAtom(1), ac.getAtom(2)), ac.getBond(ac.getAtom(3), ac.getAtom(5))}… in z_1_2_difluroethene_explicit()
483 is(new IAtom[]{ac.getAtom(0), ac.getAtom(1), ac.getAtom(3), ac.getAtom(4)})); in extendedTetrahedral_ccw()
[all …]
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| H A D | SmilesParserTest.java | 112 … assertTrue(mol.getBond(mol.getAtom(0), mol.getAtom(1)).getFlag(CDKConstants.SINGLE_OR_DOUBLE)); in testSingleOrDoubleFlag()
113 … assertTrue(mol.getBond(mol.getAtom(1), mol.getAtom(2)).getFlag(CDKConstants.SINGLE_OR_DOUBLE)); in testSingleOrDoubleFlag()
114 … assertTrue(mol.getBond(mol.getAtom(2), mol.getAtom(3)).getFlag(CDKConstants.SINGLE_OR_DOUBLE)); in testSingleOrDoubleFlag()
115 … assertTrue(mol.getBond(mol.getAtom(3), mol.getAtom(4)).getFlag(CDKConstants.SINGLE_OR_DOUBLE)); in testSingleOrDoubleFlag()
116 … assertTrue(mol.getBond(mol.getAtom(4), mol.getAtom(0)).getFlag(CDKConstants.SINGLE_OR_DOUBLE)); in testSingleOrDoubleFlag()
118 … assertFalse(mol.getBond(mol.getAtom(4), mol.getAtom(5)).getFlag(CDKConstants.SINGLE_OR_DOUBLE)); in testSingleOrDoubleFlag()
120 … assertTrue(mol.getBond(mol.getAtom(5), mol.getAtom(6)).getFlag(CDKConstants.SINGLE_OR_DOUBLE)); in testSingleOrDoubleFlag()
121 … assertTrue(mol.getBond(mol.getAtom(6), mol.getAtom(7)).getFlag(CDKConstants.SINGLE_OR_DOUBLE)); in testSingleOrDoubleFlag()
122 … assertTrue(mol.getBond(mol.getAtom(7), mol.getAtom(8)).getFlag(CDKConstants.SINGLE_OR_DOUBLE)); in testSingleOrDoubleFlag()
123 … assertTrue(mol.getBond(mol.getAtom(8), mol.getAtom(9)).getFlag(CDKConstants.SINGLE_OR_DOUBLE)); in testSingleOrDoubleFlag()
[all …]
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| /dports/science/cdk/cdk-cdk-2.3/descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/ |
| H A D | AtomTyperTests.java | 75 atom = molecule.getAtom(0); in testNonHNeighbours()
79 atom = molecule.getAtom(0); in testNonHNeighbours()
83 atom = molecule.getAtom(0); in testNonHNeighbours()
87 atom = molecule.getAtom(0); in testNonHNeighbours()
102 atom = molecule.getAtom(1); in testDoubleBondHetero()
115 atom = molecule.getAtom(0); in testCarbonylConjugated()
119 atom = molecule.getAtom(0); in testCarbonylConjugated()
132 atom = molecule.getAtom(0); in testNextToAromatic()
136 atom = molecule.getAtom(0); in testNextToAromatic()
149 atom = molecule.getAtom(0); in testGetPolarBondArray()
[all …]
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| /dports/science/cdk/cdk-cdk-2.3/base/isomorphism/src/test/java/org/openscience/cdk/isomorphism/ |
| H A D | StereoMatchTest.java | 54 … query.addStereoElement(new TetrahedralChirality(query.getAtom(0), new IAtom[]{query.getAtom(1), in tetrahedral_missingInTarget()
55 … query.getAtom(2), query.getAtom(3), query.getAtom(4)}, ITetrahedralChirality.Stereo.CLOCKWISE)); in tetrahedral_missingInTarget()
68 …target.getAtom(2), target.getAtom(3), target.getAtom(4)}, ITetrahedralChirality.Stereo.CLOCKWISE)); in tetrahedral_missingInQuery()
77 … query.getAtom(2), query.getAtom(3), query.getAtom(4)}, ITetrahedralChirality.Stereo.CLOCKWISE)); in tetrahedral_match()
79 …target.getAtom(2), target.getAtom(3), target.getAtom(4)}, ITetrahedralChirality.Stereo.CLOCKWISE)); in tetrahedral_match()
88 … query.getAtom(2), query.getAtom(3), query.getAtom(4)}, ITetrahedralChirality.Stereo.CLOCKWISE)); in tetrahedral_mismatch()
90 …target.getAtom(2), target.getAtom(3), target.getAtom(4)}, ITetrahedralChirality.Stereo.ANTI_CLOCKW… in tetrahedral_mismatch()
103 … query.getAtom(2), query.getAtom(3), query.getAtom(4)}, ITetrahedralChirality.Stereo.CLOCKWISE)); in tetrahedral_match_swap()
105 …target.getAtom(2), target.getAtom(3), target.getAtom(4)}, ITetrahedralChirality.Stereo.ANTI_CLOCKW… in tetrahedral_match_swap()
115 … query.getAtom(2), query.getAtom(3), query.getAtom(4)}, ITetrahedralChirality.Stereo.CLOCKWISE)); in tetrahedral_mismatch_swap()
[all …]
|
| /dports/science/cdk/cdk-cdk-2.3/storage/ctab/src/test/java/org/openscience/cdk/io/ |
| H A D | MDLV3000WriterTest.java | 77 mol.getAtom(0).setImplicitHydrogenCount(0); in outputFormalCharge()
78 mol.getAtom(0).setFormalCharge(-1); in outputFormalCharge()
79 mol.getAtom(1).setImplicitHydrogenCount(3); in outputFormalCharge()
91 mol.getAtom(0).setImplicitHydrogenCount(0); in outputMassNumber()
92 mol.getAtom(0).setMassNumber(2); in outputMassNumber()
115 mol.addBond(new Bond(mol.getAtom(0), mol.getAtom(1), null)); in nullBondOrder()
117 mol.getAtom(0).setMassNumber(2); in nullBondOrder()
129 mol.getAtom(0).setMassNumber(2); in unsetBondOrder()
323 sgroup.addAtom(mol.getAtom(1)); in writeSRUs()
324 sgroup.addAtom(mol.getAtom(2)); in writeSRUs()
[all …]
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| /dports/science/cdk/cdk-cdk-2.3/base/test-core/src/test/java/org/openscience/cdk/graph/ |
| H A D | ShortestPathsTest.java | 577 IAtom a = simple.getAtom(0); in testAtomsTo_Atom_Simple()
578 IAtom b = simple.getAtom(1); in testAtomsTo_Atom_Simple()
579 IAtom c = simple.getAtom(2); in testAtomsTo_Atom_Simple()
580 IAtom d = simple.getAtom(3); in testAtomsTo_Atom_Simple()
581 IAtom e = simple.getAtom(4); in testAtomsTo_Atom_Simple()
597 IAtom a = simple.getAtom(0); in testAtomsTo_Int_Simple()
598 IAtom b = simple.getAtom(1); in testAtomsTo_Int_Simple()
599 IAtom c = simple.getAtom(2); in testAtomsTo_Int_Simple()
600 IAtom d = simple.getAtom(3); in testAtomsTo_Int_Simple()
601 IAtom e = simple.getAtom(4); in testAtomsTo_Int_Simple()
[all …]
|
| /dports/science/cdk/cdk-cdk-2.3/tool/builder3d/src/test/java/org/openscience/cdk/modeling/builder3d/ |
| H A D | FurtherAtomPlacer3DTest.java | 97 … IAtom atom2 = atmplacer.getPlacedHeavyAtom(molecule, molecule.getAtom(1), molecule.getAtom(0)); in testGetPlacedHeavyAtom_IAtomContainer_IAtom_IAtom()
98 … IAtom atom3 = atmplacer.getPlacedHeavyAtom(molecule, molecule.getAtom(2), molecule.getAtom(1)); in testGetPlacedHeavyAtom_IAtomContainer_IAtom_IAtom()
99 … IAtom nullAtom = atmplacer.getPlacedHeavyAtom(molecule, molecule.getAtom(0), molecule.getAtom(1)); in testGetPlacedHeavyAtom_IAtomContainer_IAtom_IAtom()
101 Assert.assertEquals(atom2, molecule.getAtom(2)); in testGetPlacedHeavyAtom_IAtomContainer_IAtom_IAtom()
102 Assert.assertEquals(atom3, molecule.getAtom(3)); in testGetPlacedHeavyAtom_IAtomContainer_IAtom_IAtom()
117 Assert.assertEquals(atom1, molecule.getAtom(1)); in testGetPlacedHeavyAtom_IAtomContainer_IAtom()
119 Assert.assertEquals(atom2, molecule.getAtom(1)); in testGetPlacedHeavyAtom_IAtomContainer_IAtom()
153 IAtom atom0 = molecule.getAtom(0); in testGetUnplacedRingHeavyAtom_IAtomContainer_IAtom()
154 IAtom atom1 = molecule.getAtom(1); in testGetUnplacedRingHeavyAtom_IAtomContainer_IAtom()
155 IAtom natom = molecule.getAtom(4); in testGetUnplacedRingHeavyAtom_IAtomContainer_IAtom()
[all …]
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| H A D | AtomPlacer3DTest.java | 162 chain.addAtom(ac.getAtom(29)); in testFindHeavyAtomsInChain_IAtomContainer_IAtomContainer()
163 chain.addAtom(ac.getAtom(30)); in testFindHeavyAtomsInChain_IAtomContainer_IAtomContainer()
201 IAtom acplaced = new AtomPlacer3D().getPlacedHeavyAtom(ac, ac.getAtom(0), ac.getAtom(1)); in testGetPlacedHeavyAtom_IAtomContainer_IAtom_IAtom()
204 acplaced = new AtomPlacer3D().getPlacedHeavyAtom(ac, ac.getAtom(0), ac.getAtom(2)); in testGetPlacedHeavyAtom_IAtomContainer_IAtom_IAtom()
206 acplaced = new AtomPlacer3D().getPlacedHeavyAtom(ac, ac.getAtom(0), ac.getAtom(1)); in testGetPlacedHeavyAtom_IAtomContainer_IAtom_IAtom()
246 IAtom carbon = ac.getAtom(0); in testIsUnplacedHeavyAtom()
247 IAtom hydrogen = ac.getAtom(1); in testIsUnplacedHeavyAtom()
268 IAtom carbon = ac.getAtom(0); in testIsPlacedHeavyAtom()
290 IAtom carbon = ac.getAtom(0); in testIsAliphaticHeavyAtom()
312 IAtom carbon = ac.getAtom(0); in testIsRingHeavyAtom()
[all …]
|
| /dports/science/cdk/cdk-cdk-2.3/legacy/src/test/java/org/openscience/cdk/atomtype/ |
| H A D | MMFF94AtomTypeMatcherTest.java | 190 logger.debug("atomNr:" + mol.getAtom(i).toString()); in testFindMatchingAtomType_IAtomContainer_IAtom_Methanol()
224 logger.debug("atomNr:" + mol.getAtom(i).toString()); in testFindMatchingAtomType_IAtomContainer_IAtom_Methylamine()
259 logger.debug("atomNr:" + mol.getAtom(i).toString()); in testFindMatchingAtomType_IAtomContainer_IAtom_Ethoxyethane()
291 logger.debug("atomNr:" + mol.getAtom(i).toString()); in testFindMatchingAtomType_IAtomContainer_IAtom_Methanethiol()
323 logger.debug("atomNr:" + mol.getAtom(i).toString()); in testFindMatchingAtomType_IAtomContainer_IAtom_Chloromethane()
348 .newInstance(IBond.class, mol.getAtom(0), mol.getAtom(1), Order.DOUBLE); in testFindMatchingAtomType_IAtomContainer_IAtom_Benzene()
351 ringBond = builder.newInstance(IBond.class, mol.getAtom(1), mol.getAtom(2), Order.SINGLE); in testFindMatchingAtomType_IAtomContainer_IAtom_Benzene()
354 ringBond = builder.newInstance(IBond.class, mol.getAtom(2), mol.getAtom(3), Order.DOUBLE); in testFindMatchingAtomType_IAtomContainer_IAtom_Benzene()
357 ringBond = builder.newInstance(IBond.class, mol.getAtom(3), mol.getAtom(4), Order.SINGLE); in testFindMatchingAtomType_IAtomContainer_IAtom_Benzene()
360 ringBond = builder.newInstance(IBond.class, mol.getAtom(4), mol.getAtom(5), Order.DOUBLE); in testFindMatchingAtomType_IAtomContainer_IAtom_Benzene()
[all …]
|
| /dports/science/cdk/cdk-cdk-2.3/base/test-standard/src/test/java/org/openscience/cdk/geometry/ |
| H A D | BondToolsTest.java | 70 …Assert.assertFalse(BondTools.isCisTrans(mol.getAtom(2), mol.getAtom(0), mol.getAtom(1), mol.getAto… in testIsCisTrans_IAtom_IAtom_IAtom_IAtom_IAtomContainer()
80 Assert.assertFalse(BondTools.isLeft(mol.getAtom(1), mol.getAtom(0), mol.getAtom(2))); in testIsLeft_IAtom_IAtom_IAtom()
91 … BondTools.giveAngleBothMethods(mol.getAtom(0), mol.getAtom(2), mol.getAtom(3), true), 0.2); in testGiveAngleBothMethods_IAtom_IAtom_IAtom_boolean()
93 … BondTools.giveAngleBothMethods(mol.getAtom(0), mol.getAtom(2), mol.getAtom(3), false), 0.2); in testGiveAngleBothMethods_IAtom_IAtom_IAtom_boolean()
112 Assert.assertTrue(BondTools.closeEnoughToBond(mol.getAtom(0), mol.getAtom(1), 1)); in testCloseEnoughToBond_IAtom_IAtom_double()
113 Assert.assertFalse(BondTools.closeEnoughToBond(mol.getAtom(0), mol.getAtom(8), 1)); in testCloseEnoughToBond_IAtom_IAtom_double()
124 .getAtom(2).getPoint2d(), mol.getAtom(3).getPoint2d(), true), 0.2); in testGiveAngleBothMethods_Point2d_Point2d_Point2d_boolean()
126 .getAtom(2).getPoint2d(), mol.getAtom(3).getPoint2d(), false), 0.2); in testGiveAngleBothMethods_Point2d_Point2d_Point2d_boolean()
177 mol.getAtom(i).setSymbol("C"); in testIsStereo_IAtomContainer_IAtom_forinvalid()
228 …assertEquals(2.0943946986086157, BondTools.giveAngle(mol.getAtom(0), mol.getAtom(2), mol.getAtom(3… in testGiveAngle_IAtom_IAtom_IAtom()
[all …]
|
| /dports/science/cdk/cdk-cdk-2.3/tool/smarts/src/test/java/org/openscience/cdk/isomorphism/ |
| H A D | QueryStereoFilterTest.java | 68 …target.getAtom(2), target.getAtom(3), target.getAtom(4)}, ITetrahedralChirality.Stereo.CLOCKWISE)); in tetrahedral_missingInQuery()
77 …target.getAtom(2), target.getAtom(3), target.getAtom(4)}, ITetrahedralChirality.Stereo.CLOCKWISE)); in tetrahedral_match()
86 …target.getAtom(2), target.getAtom(3), target.getAtom(4)}, ITetrahedralChirality.Stereo.ANTI_CLOCKW… in tetrahedral_mismatch()
99 …target.getAtom(2), target.getAtom(3), target.getAtom(4)}, ITetrahedralChirality.Stereo.ANTI_CLOCKW… in tetrahedral_match_swap()
109 …target.getAtom(2), target.getAtom(3), target.getAtom(4)}, ITetrahedralChirality.Stereo.CLOCKWISE)); in tetrahedral_mismatch_swap()
119 …target.getAtom(2), target.getAtom(3), target.getAtom(4)}, ITetrahedralChirality.Stereo.CLOCKWISE)); in tetrahedral_unspecified_match()
129 …target.getAtom(2), target.getAtom(3), target.getAtom(4)}, ITetrahedralChirality.Stereo.ANTI_CLOCKW… in tetrahedral_unspecified_match2()
139 …target.getAtom(2), target.getAtom(3), target.getAtom(4)}, ITetrahedralChirality.Stereo.ANTI_CLOCKW… in tetrahedral_unspecified_mismatch()
149 …target.getAtom(2), target.getAtom(3), target.getAtom(4)}, ITetrahedralChirality.Stereo.CLOCKWISE)); in tetrahedral_unspecified_mismatch2()
159 …target.getAtom(2), target.getAtom(3), target.getAtom(4)}, ITetrahedralChirality.Stereo.CLOCKWISE)); in tetrahedral_either_match()
[all …]
|
| /dports/science/cdk/cdk-cdk-2.3/descriptor/cip/src/test/java/org/openscience/cdk/geometry/cip/rules/ |
| H A D | AtomicNumberRuleTest.java | 56 …Ligand ligand = new Ligand(molecule, new VisitedAtoms(), molecule.getAtom(1), molecule.getAtom(0)); in testCompare_Identity()
63 …igand ligand1 = new Ligand(molecule, new VisitedAtoms(), molecule.getAtom(1), molecule.getAtom(0)); in testCompare()
64 …igand ligand2 = new Ligand(molecule, new VisitedAtoms(), molecule.getAtom(1), molecule.getAtom(2)); in testCompare()
73 … ILigand ligand1 = new Ligand(molecule, visitedAtoms, molecule.getAtom(1), molecule.getAtom(4)); in testOrder()
74 … ILigand ligand2 = new Ligand(molecule, visitedAtoms, molecule.getAtom(1), molecule.getAtom(3)); in testOrder()
75 … ILigand ligand3 = new Ligand(molecule, visitedAtoms, molecule.getAtom(1), molecule.getAtom(2)); in testOrder()
76 … ILigand ligand4 = new Ligand(molecule, visitedAtoms, molecule.getAtom(1), molecule.getAtom(0)); in testOrder()
92 … ILigand ligand1 = new ImplicitHydrogenLigand(molecule, new VisitedAtoms(), molecule.getAtom(1)); in testImplicitHydrogen_Same()
93 …igand ligand2 = new Ligand(molecule, new VisitedAtoms(), molecule.getAtom(1), molecule.getAtom(4)); in testImplicitHydrogen_Same()
101 … ILigand ligand1 = new ImplicitHydrogenLigand(molecule, new VisitedAtoms(), molecule.getAtom(1)); in testImplicitHydrogen()
[all …]
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| H A D | MassNumberRuleTest.java | 56 …Ligand ligand = new Ligand(molecule, new VisitedAtoms(), molecule.getAtom(1), molecule.getAtom(0)); in testCompare_Identity()
63 …igand ligand1 = new Ligand(molecule, new VisitedAtoms(), molecule.getAtom(1), molecule.getAtom(0)); in testCompare()
64 …igand ligand2 = new Ligand(molecule, new VisitedAtoms(), molecule.getAtom(1), molecule.getAtom(2)); in testCompare()
73 … ILigand ligand1 = new Ligand(molecule, visitedAtoms, molecule.getAtom(1), molecule.getAtom(4)); in testOrder()
74 … ILigand ligand2 = new Ligand(molecule, visitedAtoms, molecule.getAtom(1), molecule.getAtom(3)); in testOrder()
75 … ILigand ligand3 = new Ligand(molecule, visitedAtoms, molecule.getAtom(1), molecule.getAtom(2)); in testOrder()
76 … ILigand ligand4 = new Ligand(molecule, visitedAtoms, molecule.getAtom(1), molecule.getAtom(0)); in testOrder()
95 … ILigand ligand1 = new ImplicitHydrogenLigand(molecule, new VisitedAtoms(), molecule.getAtom(1)); in testImplicitHydrogen_Same()
96 …igand ligand2 = new Ligand(molecule, new VisitedAtoms(), molecule.getAtom(1), molecule.getAtom(4)); in testImplicitHydrogen_Same()
104 … ILigand ligand1 = new ImplicitHydrogenLigand(molecule, new VisitedAtoms(), molecule.getAtom(1)); in testImplicitHydrogen()
[all …]
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| H A D | CombinedAtomicMassNumberRuleTest.java | 55 …Ligand ligand = new Ligand(molecule, new VisitedAtoms(), molecule.getAtom(1), molecule.getAtom(0)); in testCompare_Identity()
62 …igand ligand1 = new Ligand(molecule, new VisitedAtoms(), molecule.getAtom(1), molecule.getAtom(0)); in testCompare()
63 …igand ligand2 = new Ligand(molecule, new VisitedAtoms(), molecule.getAtom(1), molecule.getAtom(2)); in testCompare()
71 …igand ligand1 = new Ligand(molecule, new VisitedAtoms(), molecule.getAtom(1), molecule.getAtom(4)); in testOrder()
72 …igand ligand2 = new Ligand(molecule, new VisitedAtoms(), molecule.getAtom(1), molecule.getAtom(3)); in testOrder()
73 …igand ligand3 = new Ligand(molecule, new VisitedAtoms(), molecule.getAtom(1), molecule.getAtom(2)); in testOrder()
74 …igand ligand4 = new Ligand(molecule, new VisitedAtoms(), molecule.getAtom(1), molecule.getAtom(0)); in testOrder()
|
| H A D | CIPLigandRuleTest.java | 51 …igand ligandF = new Ligand(molecule, new VisitedAtoms(), molecule.getAtom(1), molecule.getAtom(0)); in testCBrIFCl()
52 …gand ligandBr = new Ligand(molecule, new VisitedAtoms(), molecule.getAtom(1), molecule.getAtom(2)); in testCBrIFCl()
53 …gand ligandCl = new Ligand(molecule, new VisitedAtoms(), molecule.getAtom(1), molecule.getAtom(3)); in testCBrIFCl()
54 …igand ligandI = new Ligand(molecule, new VisitedAtoms(), molecule.getAtom(1), molecule.getAtom(4)); in testCBrIFCl()
79 …Ligand ligand = new Ligand(molecule, new VisitedAtoms(), molecule.getAtom(1), molecule.getAtom(0)); in testCompare_Identity()
87 …igand ligand1 = new Ligand(molecule, new VisitedAtoms(), molecule.getAtom(1), molecule.getAtom(0)); in testCompare()
88 …igand ligand2 = new Ligand(molecule, new VisitedAtoms(), molecule.getAtom(1), molecule.getAtom(2)); in testCompare()
170 … ILigand ligand1 = new ImplicitHydrogenLigand(molecule, new VisitedAtoms(), molecule.getAtom(1)); in testImplicitHydrogen_Same()
171 …igand ligand2 = new Ligand(molecule, new VisitedAtoms(), molecule.getAtom(1), molecule.getAtom(4)); in testImplicitHydrogen_Same()
181 …igand ligand2 = new Ligand(molecule, new VisitedAtoms(), molecule.getAtom(1), molecule.getAtom(3)); in testImplicitHydrogen()
[all …]
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| /dports/science/openbabel/openbabel-3.1.1/src/ |
| H A D | mcdlutil.cpp | 1067 r1=getAtom(aT)->rx-getAtom(aN)->rx; in unitVectorCoincident()
1068 r2=getAtom(aT)->ry-getAtom(aN)->ry; in unitVectorCoincident()
1103 r1=getAtom(aT)->rx-getAtom(aN)->rx; in unitVector()
1104 r2=getAtom(aT)->ry-getAtom(aN)->ry; in unitVector()
1431 x=getAtom(k1)->rx-getAtom(k2)->rx; in bondLength()
1432 y=getAtom(k1)->ry-getAtom(k2)->ry; in bondLength()
1953 if ((getAtom(na1)->rx==getAtom(na2)->rx) && (getAtom(na1)->ry==getAtom(na2)->ry)) { in twoAtomUnitVector()
2724 x1=getAtom(an)->rx-getAtom(n)->rx; in atomDistanceMetric()
2725 y1=getAtom(an)->ry-getAtom(n)->ry; in atomDistanceMetric()
2728 x2=getAtom(i)->rx-getAtom(n)->rx; in atomDistanceMetric()
[all …]
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| /dports/science/cdk/cdk-cdk-2.3/legacy/src/main/java/org/openscience/cdk/iupac/parser/ |
| H A D | MoleculeBuilder.java | 166 addAtom("O", currentMolecule.getAtom(addPos), IBond.Order.SINGLE, 1); in addFunGroup()
200 addAtom("F", currentMolecule.getAtom(addPos), IBond.Order.SINGLE, 0); in addFunGroup()
218 addAtom("I", currentMolecule.getAtom(addPos), IBond.Order.SINGLE, 0); in addFunGroup()
227 addAtom("N", currentMolecule.getAtom(addPos), IBond.Order.SINGLE, 0); in addFunGroup()
266 benzene.getAtom(0)); in addFunGroup()
269 benzene.getAtom(0)); in addFunGroup()
304 endOfChain = currentMolecule.getAtom(currentMolecule.getAtomCount()); in addFunGroup()
310 endOfChain = currentMolecule.getAtom(currentMolecule.getAtomCount()); in addFunGroup()
317 endOfChain = currentMolecule.getAtom(currentMolecule.getAtomCount()); in addFunGroup()
328 endOfChain = currentMolecule.getAtom(currentMolecule.getAtomCount()); in addFunGroup()
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| /dports/science/cdk/cdk-cdk-2.3/base/reaction/src/test/java/org/openscience/cdk/reaction/type/ |
| H A D | RadicalSiteRrAlphaReactionTest.java | 87 molecule.getAtom(0).setFlag(CDKConstants.REACTIVE_CENTER, true); in testInitiate_IAtomContainerSet_IAtomContainerSet()
129 molecule.getAtom(3).setFormalCharge(1); in getExampleReactants()
144 molecule.getAtom(3).setFormalCharge(0); in getExampleReactants()
167 molecule.getAtom(0).setFormalCharge(1); in getExpectedProducts()
187 molecule.getAtom(0).setFormalCharge(0); in getExpectedProducts()
272 molecule.getAtom(0)); in testMapping()
273 Assert.assertEquals(mappedProductA1, product.getAtom(0)); in testMapping()
275 molecule.getAtom(1)); in testMapping()
276 Assert.assertEquals(mappedProductA2, product.getAtom(1)); in testMapping()
278 molecule.getAtom(3)); in testMapping()
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| H A D | RadicalSiteRrBetaReactionTest.java | 86 molecule.getAtom(0).setFlag(CDKConstants.REACTIVE_CENTER, true); in testInitiate_IAtomContainerSet_IAtomContainerSet()
130 molecule.getAtom(4).setFormalCharge(1); in getExampleReactants()
143 molecule.getAtom(4).setFormalCharge(0); in getExampleReactants()
166 molecule.getAtom(0).setFormalCharge(1); in getExpectedProducts()
186 molecule.getAtom(0).setFormalCharge(0); in getExpectedProducts()
271 molecule.getAtom(0)); in testMapping()
272 Assert.assertEquals(mappedProductA1, product.getAtom(0)); in testMapping()
274 molecule.getAtom(1)); in testMapping()
275 Assert.assertEquals(mappedProductA2, product.getAtom(1)); in testMapping()
277 molecule.getAtom(4)); in testMapping()
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| H A D | RadicalSiteRrGammaReactionTest.java | 87 molecule.getAtom(0).setFlag(CDKConstants.REACTIVE_CENTER, true); in testInitiate_IAtomContainerSet_IAtomContainerSet()
133 molecule.getAtom(5).setFormalCharge(1); in getExampleReactants()
144 molecule.getAtom(5).setFormalCharge(0); in getExampleReactants()
167 molecule.getAtom(0).setFormalCharge(1); in getExpectedProducts()
187 molecule.getAtom(0).setFormalCharge(0); in getExpectedProducts()
272 molecule.getAtom(0)); in testMapping()
273 Assert.assertEquals(mappedProductA1, product.getAtom(0)); in testMapping()
275 molecule.getAtom(1)); in testMapping()
276 Assert.assertEquals(mappedProductA2, product.getAtom(1)); in testMapping()
278 molecule.getAtom(5)); in testMapping()
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| H A D | RadicalSiteRrDeltaReactionTest.java | 87 molecule.getAtom(0).setFlag(CDKConstants.REACTIVE_CENTER, true); in testInitiate_IAtomContainerSet_IAtomContainerSet()
130 molecule.getAtom(6).setFormalCharge(1); in getExampleReactants()
139 molecule.getAtom(6).setFormalCharge(0); in getExampleReactants()
162 molecule.getAtom(0).setFormalCharge(1); in getExpectedProducts()
182 molecule.getAtom(0).setFormalCharge(0); in getExpectedProducts()
272 molecule.getAtom(0)); in testMapping()
273 Assert.assertEquals(mappedProductA1, product.getAtom(0)); in testMapping()
275 molecule.getAtom(1)); in testMapping()
276 Assert.assertEquals(mappedProductA2, product.getAtom(1)); in testMapping()
278 molecule.getAtom(6)); in testMapping()
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| /dports/science/cdk/cdk-cdk-2.3/descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/ |
| H A D | IsProtonInAromaticSystemDescriptorTest.java | 57 assertThat(mol.getAtom(11).getSymbol(), is("H")); in testIsProtonInAromaticSystemDescriptor()
58 assertThat(mol.getAtom(12).getSymbol(), is("H")); in testIsProtonInAromaticSystemDescriptor()
59 assertThat(mol.getAtom(13).getSymbol(), is("H")); in testIsProtonInAromaticSystemDescriptor()
60 assertThat(mol.getAtom(14).getSymbol(), is("H")); in testIsProtonInAromaticSystemDescriptor()
61 assertThat(mol.getAtom(15).getSymbol(), is("H")); in testIsProtonInAromaticSystemDescriptor()
62 assertThat(mol.getAtom(16).getSymbol(), is("H")); in testIsProtonInAromaticSystemDescriptor()
63 …Assert.assertEquals(0, ((IntegerResult) descriptor.calculate(mol.getAtom(11), mol).getValue()).int… in testIsProtonInAromaticSystemDescriptor()
64 …Assert.assertEquals(1, ((IntegerResult) descriptor.calculate(mol.getAtom(12), mol).getValue()).int… in testIsProtonInAromaticSystemDescriptor()
65 …Assert.assertEquals(0, ((IntegerResult) descriptor.calculate(mol.getAtom(13), mol).getValue()).int… in testIsProtonInAromaticSystemDescriptor()
66 …Assert.assertEquals(0, ((IntegerResult) descriptor.calculate(mol.getAtom(14), mol).getValue()).int… in testIsProtonInAromaticSystemDescriptor()
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| /dports/science/cdk/cdk-cdk-2.3/descriptor/cip/src/test/java/org/openscience/cdk/geometry/cip/ |
| H A D | LigandTest.java | 42 …Ligand ligand = new Ligand(molecule, new VisitedAtoms(), molecule.getAtom(1), molecule.getAtom(0)); in testConstructorAndGetMethods()
45 Assert.assertEquals(molecule.getAtom(1), ligand.getCentralAtom()); in testConstructorAndGetMethods()
46 Assert.assertEquals(molecule.getAtom(0), ligand.getLigandAtom()); in testConstructorAndGetMethods()
54 …Ligand ligand = new Ligand(molecule, new VisitedAtoms(), molecule.getAtom(1), molecule.getAtom(0)); in testVisitedTracking()
55 Assert.assertTrue(ligand.getVisitedAtoms().isVisited(molecule.getAtom(1))); in testVisitedTracking()
56 Assert.assertTrue(ligand.isVisited(molecule.getAtom(1))); in testVisitedTracking()
57 Assert.assertFalse(ligand.getVisitedAtoms().isVisited(molecule.getAtom(0))); in testVisitedTracking()
58 Assert.assertFalse(ligand.isVisited(molecule.getAtom(0))); in testVisitedTracking()
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| /dports/science/cdk/cdk-cdk-2.3/tool/sdg/src/test/java/org/openscience/cdk/layout/ |
| H A D | NonPlanarBondsTest.java | 78 …m.addStereoElement(new TetrahedralChirality(m.getAtom(0), new IAtom[]{m.getAtom(0), m.getAtom(1), … in clockwise_implH_1()
100 …m.addStereoElement(new TetrahedralChirality(m.getAtom(0), new IAtom[]{m.getAtom(0), m.getAtom(1), … in clockwise_implH_2()
120 …m.addStereoElement(new TetrahedralChirality(m.getAtom(0), new IAtom[]{m.getAtom(0), m.getAtom(1), … in anticlockwise_implH_1()
142 …m.addStereoElement(new TetrahedralChirality(m.getAtom(0), new IAtom[]{m.getAtom(0), m.getAtom(1), … in anticlockwise_implH_2()
168 …m.addStereoElement(new TetrahedralChirality(m.getAtom(0), new IAtom[]{m.getAtom(1), m.getAtom(4), … in clockwise_1()
197 …m.addStereoElement(new TetrahedralChirality(m.getAtom(0), new IAtom[]{m.getAtom(1), m.getAtom(4), … in clockwise_2()
223 …m.addStereoElement(new TetrahedralChirality(m.getAtom(0), new IAtom[]{m.getAtom(1), m.getAtom(4), … in anticlockwise_1()
252 …m.addStereoElement(new TetrahedralChirality(m.getAtom(0), new IAtom[]{m.getAtom(1), m.getAtom(4), … in anticlockwise_2()
277 …m.addStereoElement(new ExtendedTetrahedral(m.getAtom(2), new IAtom[]{m.getAtom(0), m.getAtom(6), m… in nonPlanarBondsForAntiClockwsieExtendedTetrahedral()
300 …m.addStereoElement(new ExtendedTetrahedral(m.getAtom(2), new IAtom[]{m.getAtom(0), m.getAtom(6), m… in nonPlanarBondsForClockwsieExtendedTetrahedral()
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